view calc_cnsegements_titan.xml @ 0:c6e48c6ac606 draft default tip

planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty

<tool id="calc_cnsegments" name="calc_cnsegements" version="0.0.1">
  <description>
    Calculate Copy Number Segments from TITAN output
  </description>
  <command>
    <![CDATA[
    perl $__tool_directory__/calc_cnsegements_titan.pl

      #if $sampleid_source.sampleid_selector == "bamfile":
        -id \$(basename $sampleid_source.sample_id | sed 's/.bam$//g' )
      #else:
        -id $sampleid_source.sample_id
      #end if

     -o $outfile
     -s $symmetric
     -igv $outIGV
     -i $infile

    ]]>
  </command>
  <inputs>
    <conditional name="sampleid_source">
      <param label="Choose the source to open the Sample Id" name="sampleid_selector" type="select">
        <option value="bamfile">Bam File Name</option>
        <option value="manual">Manual</option>
      </param>
      <when value="bamfile">
        <param type="data" format="bam" name="sample_id" label="Sequence Alignment File"/>
      </when>
      <when value="manual">
        <param name="sample_id" type="text" label="Sample ID (Name)"/>
      </when>
    </conditional>
    <param type="data" format="txt" name="infile" label="SNP Summary Information (TITAN Output)"/>
    <param type="boolean" name="symmetric" label="Symmetric" checked="yes" truevalue="1" falsevalue="0"/>
  </inputs>
  <outputs>
    <data format="txt" name="outfile"/>
    <data format="seg" name="outIGV"/>
  </outputs>
</tool>